CD58 encodes for a glycosylated cell adhesion molecule known as lymphocyte-associated antigen 3(LFA3) that is found on human chromosome 1p13. It is present on the surface of antigen-presenting cells (APCs), especially macrophages, and is able to promote their specific adherence to the CD2 ligand on the T-cell surface. A whole-genome association scan has proposed that genetic variations in CD58 are associated with MS risk. The most studied genetic variant is rs2300747, where inconclusive data were shown; an association was maintained in different studies [16-18] and supported by the fact that MS patients carrying the G protective allele presented higher CD58 mRNA expression level during clinical remission [17]. However, this genetic variant association with MS was not consistent among other studies [19, 20]. On the other hand, a second genetic variant rs12044852 was shown to be correlated with MS in Australians and Russians [18, 21] but not in Malay and Iranian [19, 22] populations where the CC genotype was strongly associated with multiple sclerosis severity score (MSSS), indicating by this a negative effect of this SNP in response to interferon-beta (IFN-β) therapy [22].

CD6 encodes a cell surface scavenger implicated in thymocyte differentiation as well as in T-cell activation and differentiation. It has been suggested that CD6 may play a crucial role in MS pathogenesis as it was shown to be involved in the transmigration of leukocytes across the blood-brain barrier (BBB). However, its definite role in regulating T-cell responses remains controversial. Genome-wide association studies have identified a large number of genetic variants associated with autoimmune diseases, including MS. Previous reports showed an association between CD6 genetic variant rs17824933 and MS [23-25]. In addition, the risk allele of this single nucleotide polymorphism (SNP) was demonstrated to be associated with a decreased expression of full-length CD6 in CD4+ and CD8+ T cells, affecting consequently their proliferation [26]. Hence, targeting CD6 by developing anti-human CD6 monoclonal antibody would be of high interest in MS therapy as it prevents T cell depletion [27]. Additional risk variants were shown to be associated with MS like rs12360861 in Poland population and rs650258 in the Spanish-Basque population [28, 29] with data replication needed. Overall, these data reinforce the important role of CD6 in MS pathogenesis.

C-type lectins are key players in immune regulation as they drive different functions of antigen presenting cells (APCs) [30]. Located on chromosome 16p13, a susceptible locus for various autoimmune diseases, this gene is considered among the first non-HLA genes associated with MS [21, 31-33]. Moreover, upregulation of CLEC16A was observed in T cells of MS patients homozygous for the risk allele rs12927355 CLEC16A [34]. Additionally, higher expression of CLEC16A was detected in the white matter of MS patients, especially in the peripheral blood mononuclear cells (PBMCs). The high expression of this gene was blunted when patients were treated with vitamin D, indicating by this that CLEC16A may play a pivotal role in MS pathogenesis [11]. Additional functional studies are required to better understand the role of CLEC16A in MS as well as in other autoimmune diseases.

CYP27B1, located on chromosome 12q13-14, encodes for vitamin D metabolizing enzyme, the hydroxyvitamin D₃-1-alpha-hydroxylase. Pre-vitamin D₃ is produced in the skin and converted to 25(OH)D₃ in the liver. In skin, kidney and immune cells, CYP27B1 enzyme converts 25(OH)D₃ into 1,25 (OH)₂D₃ that binds to the vitamin D receptor present at the surface of T-cells and antigen presenting cells (APCs). Consequently, it suppresses the adaptive immune response, decreases dendritic cell and T-cell proliferation, differentiation, and maturation as well as Th1/Th2 ratio, and enhances the suppressive function of regulatory T-cells. Several studies have highlighted the role of rs703842 in MS with inconsistent results reported. Most studies showed an association between this risk variant and MS in Caucasian [35, 36], Slovakian [37], and Han Chinese [12] populations but not in others [38-40]. This was associated with a lower level of vitamin D registered in MS patients compared with controls, regardless of the risky genotypic and allelic status of this variant [35, 38]. One additional risk variant, rs118204009 was suggested to be implicated in MS [12, 41]. Further consideration of distinct ethnicity groups is needed for a better understanding of CYP27B1 role in MS.

FoxP3 encodes a transcription factor that is predominantly expressed in CD4(+) CD25(+) regulatory T cells, playing a key role in maintaining immune homeostasis. It is considered the master transcription factor of these cells, responsible for the polarization of naïve T cells into Treg cells. Recently, T regulatory (Treg) cells have been known to present an impaired suppressive function in MS disease [42]. Accumulating evidence showed that functional alterations in FoxP3 gene expression have been observed in several autoimmune diseases [43, 44], linking thereby the defect in functional peripheral immunomodulation to an established genetic variant implicated in immune regulation and autoimmunity. A positive correlation was found between the genetic variant rs3761548 and MS [44-48]. Additional single nucleotide polymorphisms were also investigated with conflicting results [47, 50]. FoxP3 gene expression level was validated to be decreased in experimental autoimmune encephalomyelitis (EAE) models or in MS patients [51-53], which could not be reproduced in the study of Akbari et al. [54]. Interestingly, FoxP3 expression level could be restored by (IFN-β) treatment [55] or through injection of ex vivo autologous Treg cells that helped in increasing the level of Treg in patients’ blood. To sum up, FoxP3 could share a powerful link to MS susceptibility as it exerts an immunomodulatory effect.

Fig. (1). This figure represents a functional analysis of the main non-HLA MS susceptible genes and their potential contribution to MS. The risk allele rs703842 of CYP27B1 induces a reduced production of IL2. Those of CD6 (rs17824933 and rs12360861) induce a decrease in CD6 expression and that of IL7-Rα (rs6897932) leads to the production of the soluble form of IL7-Rα. All four SNPs (rs703842, rs17824933, rs12360861, and rs6897932) result in the alteration of T cell proliferation that could affect MS susceptibility. The risk allele rs12044852 of CD58 induces a decrease in CD58 expression that leads to FoxP3 down-regulation. FoxP3 expression may also be down-regulated due to the risk allele rs3761548 of FoxP3. The reduced expression of FoxP3 ends up with the dysfunction of regulatory T (Treg) cells that will increase the risk for MS susceptibility. On the contrary, the protective allele (rs2300747) of CD58 induces an increase in CD58 expression that will lead to FoxP3 up-regulation and consequently to Treg cell activation, reducing the risk for MS susceptibility. The numbers in brackets above each box represent the references used in linking the main non-HLA gene SNPs studied to their gene expression level and their potential contribution to MS.

IL2-Rα, also known as CD25, is located on chromosome 10 and encodes the specific component of the high affinity IL2-R system that is implicated in autoimmunity and immune-regulation, where IL2/IL2-R signaling pathway allows the proliferation and survival of affected T cells and regulatory T cells production [56, 57]. Genome wide-association studies and fine mapping have revealed a tight link between SNPs in IL2-Rα and increased risk of immune mediated diseases including MS. Different studies were conducted on IL2-Rα polymorphisms and MS, mostly studying SNP rs2104286 that showed a risk susceptibility for the disease according to several publications [21, 58-61]. Additionally, one report has found that this SNP was accompanied by a reduced frequency of CD25(+) follicular helper T1 (TFH1) cells in patients carrying the risk genotype [62]. Fewer studies were performed on the rs12722489 SNP that also showed to be implicated with MS [59, 63]. However, data replication is needed on various populations for further validation. Furthermore, a study by Ainiding et al. showed that DNA hypo-methylation of IL2-Rα was significantly associated with MS and was accompanied by a higher expression of IL2-Rα in T cells of MS patients [64]. Together, these data confirm the tight correlation between IL2-Rα and MS.

IL7-Rα, located on 5p13 human chromosome, encodes a subunit of IL7 receptor that plays a role in immune homeostasis by assisting in the maturation of B and T cells. Various genome wide association studies revealed that IL7-Rα is correlated with various immunological disorders [65], such as MS [66], and thus is considered among the top listed candidate genes implicated in MS. Evidence illustrates the tight association between MS and SNPs in the promoter and exon region of IL7-Rα. Genotyping of 123 SNPs in 66 genes chosen according to their chromosomal location or biological roles has identified that IL7-R includes at least 3 significantly associated SNPs with MS risk [67]. Additionally, alteration in the expression of genes encoding IL7-Rα and its IL7 ligand has been shown in the cerebrospinal fluid (CSF) compartment of MS patients [68]. Most studies tackled the association between genetic variant located in exon 6 of IL7-Rα and MS with a well-established association [63, 69-77] or association reach-ing significance after stratification analysis in progressive MS subjects only [78, 79] or more specifically in secondary- progressive MS (SPMS) [80]. However, no association was found in other studies [81-83]. It has been suggested that rs6897932 risk variant is linked to altered alternative splicing of exon 6 that contributes to its skipping, affecting therefore, the ratios of soluble (sIL7- Rα) to membrane-bound IL7-Rα [84]. However, a reduced expression of sIL7-Rα was detected in progressive MS subjects regardless of their genotypes [78] and showed no effect of genotype or protein isoforms expression on MS phenotype [71]. Furthermore, a genetic variant in the 5’UTR of the RNA helicase DDX39B, a potent activator of exon 6 of IL7-Rα, was shown to reduce its translation, resulting in increased levels of the soluble form of IL7-Rα [85-88]. A meta-analysis study consisting of 9734 cases and 10436 controls confirmed the association between 3 SNPs of IL7-Rα (rs3194051 in exon 8, rs987107 in the intronic region, and rs11567686 in the promoter) and MS [66]. To sum up, IL7-Rα locus polymorphisms can have a key role in MS predisposition.

Fig. (1) depicts a functional analysis of the main non-HLA MS susceptible genes and their potential contribution to MS.